Nma_alignment_v31

!xmipp_nma_alignment (v3.1)

Usage

Align images with an atomic or pseudo-atomic (from EM volume) structure by computing deformation amplitudes along normal modes, three Euler angles, and two in-plane shifts See here for further information about the parameters of this program.

Parameters

$``: Metadata with image filenames $--mode <modeoverwrite> where <mode> can be:

• • $--label <image_labelimage> $-o, --output <output_file> $--save_metadata_stack <output_md> $: Store the original image filename in the output metadata in column imageOriginal. $: Preserve the columns from the input metadata. Some of the column values can be changed by the program. $: Reference atomic or pseudo-atomic structure in PDB format $`--odir <outputDir`.> $: Resume processing

Generation of the deformed reference volumes $: File with a list of mode filenames $`--sampling_rate <Ts`1> $`--filterVol <cutoff`15.> $: Center the PDB structure $--fixed_Gaussian <std-1>

Combined elastic and rigid-body alignment $--trustradius_scale <s1> $--mask <m> $``: Real-space instead of wavelet-space (default) projection matching (global matching) that is refined by local (Fourier central slice) projection matching Note that wavelet-based method needs the image size to be power of 2 $--discrAngStep <ang10> $`--gaussian_Fourier &lt;s`0.5&gt; $`--gaussian_Real <s`0.5> $`--zerofreq_weight <s`0.>

Examples and notes

xmipp_nma_alignment -i images.sel --pdb 2tbv.pdb --modes modelist.xmd --trustradius_scale 1.2 --sampling_rate 3.2 -o output.xmd --resume

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